dishevelled.org venn-cytoscape-plugin provides Venn and Euler diagrams for Cytoscape  as a plugin. The Venn and Euler diagram Cytoscape plugin requires java version 1.6 or later and Cytoscape version 2.7.0 or later.
The plugin provides a diagram view and a details view for comparing two or more Cytoscape groups at a time.
The diagram view is an interactive Venn or Euler diagram showing the number of nodes in each logical grouping. Clicking on any area in the diagram selects the corresponding nodes in the current Cytoscape network view. The diagram can be exported to an image file in PNG and SVG formats.
The Venn diagram view uses a symmetrical layout that supports two to four Cytoscape groups. Venn diagram views for two and three Cytoscape groups use two and three circles respectively. For four Cytoscape groups, a symmetrical construction of four ellipses is used.
The Euler diagram view uses an area-proportional layout that supports two or more Cytoscape groups. A Euler diagram is similar to a Venn diagram but does not display all possible intersections. The Euler layout allows an exact area-proportional Venn or Euler diagram to be generated when the data allow it and a statistically-justified approximation of a Venn or Euler diagram when the data do not [2, 3].
The details view shows the nodes in each logical grouping. The selection model of the details view synchronizes the selection for all of the list views (i.e. selecting a node in any one list will select it in all lists) and exports the selection to the current Cytoscape network view (selecting a node in the details view will select it in the current Cytoscape network view, but not vice versa). The details view supports two to four Cytoscape groups.
Screenshot showing the venn diagram and detail views for comparing two groups:
Screenshot showing the venn diagram and detail views for comparing three groups:
Screenshot showing the venn diagram and detail views for comparing four groups:
Screencast demonstrating the venn diagram views and interactions with the group plugin:
The Venn and Euler diagram Cytoscape plugin is available for download via the SourceForge project download page
 Leland Wilkinson, "Exact and Approximate Area-Proportional Circular Venn and Euler Diagrams," IEEE Transactions on Visualization and Computer Graphics, pp. 321-331, February, 2012